SODECL

SODECL is a library of ordinary differential equation (ODE) and stochastic differential equation (SDE) solvers in OpenCL. Using SODECL the user can calculate the integration orbits of a ODE or SDE system for a large number of different parameter values.

One example of the usefullness of SODECL is the fitting an ODE system representing a biological model to experimental data. When optimising an ODE biological model using for example genetic algorithms the ODE model has to be calculated for a large number of different parameter values combinations. SODECL accelerates the calculation of these ODE model orbit integrations by taking advantage of all the cores of a CPU or the parallel capabilities of a GPU.

Getting Started

These instructions will get you a copy of the project up and running on your local machine for development and testing purposes.

Prerequisites

To get the code you will need git. To install git on Ubuntu use the following commands in a terminal

sudo apt update
sudo apt install git

To clone the repository from github use the following command in a terminal

git clone https://github.com/avramidis/sodecl.git

You will need pybind11, to clone the repository in the sodecl folder use the following commands in a terminal

cd sodecl
git submodule update --init

You will need lsb-core, to install it you the following command in a terminal

sudo apt install lsb-core

You will need the OpenCL Runtime for Intel Core and Intel Xeon Processors to run SODECL on an Intel CPU. The runtime can be downloaded from https://software.intel.com/en-us/articles/opencl-drivers#latest_CPU_runtime. In the folder with the downloaded tgz file use the following commands in a terminal

tar -zxvf l_opencl_p_18.1.0.014.tgz
cd l_opencl_p_18.1.0.014
sudo ./install_GUI.sh

You will need to install the OpenCL library. To do that use the following commands in a terminal

sudo apt install ocl-icd-opencl-dev

To generate the makefile for compiling SODECL you will need cmake. To install cmake on Ubuntu use the following command in a terminal

sudo apt install cmake

To use the Python wrapper a number of module must be installed. To install these modules use the following commands in a terminal

sudo apt install python3-numpy
sudo pip3 install numpy
sudo pip3 install matplotlib

Installing

A step by step series of examples that tell you have to get a development env running

To generate the makefiles use the following commands in a terminal in the sodecl folders

mkdir build
cd build
cmake ..

To build SODECL use the following command

make

To run an example using the Python wrapper use the following commands in a terminal the build directory

cd examples
python3 kuramoto_euler_stochastic.py

If the run was successful the output will be similar to the following

Compute results runtime: 0.0690873 sec.
Simulation execution time:  0.5892870426177979  seconds.

Using the following command in a terminal in the pythonwrapper directory the log generated by the SODECL run can be viewed

more sodecllog.txt

The output for a successful run should be similar too the following. The log file includes the OpenCL platforms and devices available in the system. Also, it includes the build options for the OpenCL kernel and the runtime.

The platform name is Intel(R) OpenCL
	The platform version is OpenCL 1.2 LINUX
	The device name is Intel(R) Core(TM) i7-4790K CPU @ 4.00GHz
Selected platform name: Intel(R) OpenCL
Selected device name: Intel(R) Core(TM) i7-4790K CPU @ 4.00GHz
Selected device OpenCL version: OpenCL 1.2 (Build 37)
kernels/stochasticeuler.cl
Build options string: -I. -cl-fast-relaxed-math -cl-std=CL2.0 
The local group size is: 8
Compute results runtime: 0.0690873sec.

Current fixed step solvers

Euler
Runge-Kutta
Implicit Euler
Implicit midpoint
Euler-Maruyama

Simple wrappers for

Python

Future work

More ODE and SDE solvers
Variable step ODE solvers
Benchmarks
Support for using multiple devices (e.g. CPUs+GPUs)
Optimisation for AMD and NVIDIA GPUs
Tutorials
Doxygen documentation

License

This project is licensed under the MIT License - see the LICENSE file for details

How to cite SODECL

To cite SODECL please cite the URL and the DOI of the release version you used. The DOI of the latest release is at the badge at the top of this README.md file.

Acknowledgements

The Random123 library found at https://www.deshawresearch.com/resources_random123.html is used
The Catch2 unit testing library found at https://github.com/catchorg/Catch2 is used
The pybind11 library found at https://github.com/pybind/pybind11 is used
This readme file is based on the template found at https://gist.github.com/PurpleBooth/109311bb0361f32d87a2
The initial work on this library was done as part of a PhD work presented in the publication Avramidis, Eleftherios, and Ozgur E. Akman. "Optimisation of an exemplar oculomotor model using multi-objective genetic algorithms executed on a GPU-CPU combination." BMC systems Biology 11.1 (2017): 40. DOI: 10.1186/s12918-017-0416-2

avramidis / sodecl